Activating the Zygotic Genome: The Interplay between Transcription Factors, Epigenetic Modifiers, and cis-Regulatory Modules

During early animal development, maternal mRNAs and proteins direct the biosynthetic activities of embryos. Through the maternal-to-zygotic transition, when both maternal clearance and zygotic genome activation (ZGA) occur, the zygote takes over the control of its developmental programs. ZGA, accompanied by epigenetic remodeling, is coordinated by the interplay between maternal transcription factors, epigenetic modifiers, and cis-regulatory modules. How such interactions are orchestrated within a chromatin environment to ensure proper embryogenesis is a fundamental issue in biology. Understanding mechanisms that underlie genome activation will advance applications in cellular reprogramming in culture, diagnosis of diseases, and therapeutic development.Here, I uncovered the protein-protein interaction network of Foxh1, which is a maternal transcription factor functioning in Xenopus mesendoderm development. Proteomic analyses revealed that Foxh1 interacts with both positive and negative regulators, suggesting a dual role for Foxh1 in regulating zygotic transcription. My findings infer a mechanism by which Foxh1 recruits repressive epigenetic complexes to suppress mesendodermal genes in developing ectoderm. Next, I conducted genome-wide analyses of Hdac1, an enzyme that removes acetyl groups from acetylated histones, in early Xenopus embryos. My results revealed a dual function model of Hdac1. On the one hand, Hdac1 keeps inactive chromatin free of histone acetylation resulting in the spatial and temporal repression of developmental genes. On the other hand, Hdac1 participates in dynamic histone acetylation-deacetylation cycles on active chromatin, sustaining gene expression in different germ layers. Thus, Hdac1 controls embryonic cell identity through epigenetic regulations. Lastly, I developed a high-throughput screening protocol to identify functional cis-regulatory modules in Xenopus embryos by modifying STARR-seq method. My results demonstrated that the activities of candidate cis-regulatory modules can be effectively and quantitatively assessed; however, the complexity of cis-regulatory modules needs to be further determined. This modified protocol provides a basis to examine functional enhancers during ZGA in vivo. My work illustrates a complex regulation of ZGA by transcription factors, epigenetic modifiers, and cis-regulatory modules. The findings presented here will have broad impacts on developmental biology, stem cell biology, and human diseases